ETNK1

protein-coding

ethanolamine kinase 1

Gene summary

This gene encodes an ethanolamine kinase, which functions in the first committed step of the phosphatidylethanolamine synthesis pathway. This cytosolic enzyme is specific for ethanolamine and exhibits negligible kinase activity on choline. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018638.5

Inheritance

—

ClinVar variants

U:35

Top phenotype

Teratoma

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr12:22,625,075-22,690,665

External References & Databases

Ensembl (ENSG00000139163)

Transcript & Mutation Effects

hg38 • Region Span ~65.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ETNK1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 32

TeratomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018638.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	35	0	0	35

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018638.5	RefSeq	NP_061108.3	8	MANE Select
ENST00000266517.9	Ensembl	ENSP00000266517.4	8	MANE Select
NM_001039481.2	RefSeq	NP_001034570.2	3	Standard
ENST00000335148.8	Ensembl	ENSP00000334041.4	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerophospholipid metabolism - Homo sapiens (human)
Kennedy pathway from Sphingolipids
One carbon metabolism and related pathways
Metabolism of lipids
Metabolism

Biological Process

phosphatidylethanolamine biosynthetic process
phosphorylation

Molecular Function

ethanolamine kinase activity
protein binding
ATP binding

Cellular Component

nucleoplasm
cytosol
plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266517
Coding exons: 8
Length: 65591
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125748
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.91	161	245	0.656	0.0000115	2930
Missense (PolyPhen)		30	88.175	0.34023		1123
Synonymous	-0.0325	95	94.6	1.00	0.00000438	875
Loss of Function	3.70	3	21.5	0.139	0.00000105	242

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000078	0.000062	rare
Latino/Admixed American	0.00037	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000055	0.000046	rare
European (Non-Finnish)	0.000049	0.000044	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Highly specific for ethanolamine phosphorylation. May be a rate-controlling step in phosphatidylethanolamine biosynthesis.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.292
RVIS EVS: 0.04
RVIS percentile EVS: 56.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.992

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium